The quills on the hunters back are about as mysterious as anything. Why are they there? When the hunters aren't looking for you they stand at full height and their quills fall back. Then they stand strait up and quiver when the hunter contracts back for a few seconds. I speculate that these could be good for sensory items. Particularly for detecting fine vibrations in the air, like movement or breathing. I think it would be redundant for them to be a defensive mechanism, and I don't think they're for communication (although that is possible).

Halo: The Flood does point out the apparent use of the "razor sharp spines' as weapons, much to the surprise of many. Personally, I think the Hunters could stand to learn how to perform a quick backhand sooner than utilize their 'back-stabbers' :P